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- PDB-3vbr: Crystal structure of formaldehyde treated empty human Enterovirus... -

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Basic information

Entry
Database: PDB / ID: 3vbr
TitleCrystal structure of formaldehyde treated empty human Enterovirus 71 particle (room temperature)
Components
  • Genome Polyprotein, capsid protein VP0
  • Genome Polyprotein, capsid protein VP1
  • Genome Polyprotein, capsid protein VP3
KeywordsVIRUS / hand-foot-and-mouth disease / enterovirus uncoating / pocket factor / adaptor-sensor / icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 ...Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsWang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. ...Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D.I. / Fry, E.E. / Rao, Z.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.
Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D. ...Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D.I. / Fry, E.E. / Rao, Z.
History
DepositionJan 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3May 2, 2012Group: Database references
Revision 1.4May 9, 2012Group: Other
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP0
C: Genome Polyprotein, capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)77,4613
Polymers77,4613
Non-polymers00
Water00
1
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP0
C: Genome Polyprotein, capsid protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)4,647,659180
Polymers4,647,659180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP0
C: Genome Polyprotein, capsid protein VP3
x 5


  • icosahedral pentamer
  • 387 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)387,30515
Polymers387,30515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP0
C: Genome Polyprotein, capsid protein VP3
x 6


  • icosahedral 23 hexamer
  • 465 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)464,76618
Polymers464,76618
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP0
C: Genome Polyprotein, capsid protein VP3
x 5


  • crystal asymmetric unit, crystal frame
  • 387 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)387,30515
Polymers387,30515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)354.900, 354.900, 354.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017)
3generate(-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5)
4generate(-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5)
5generate(0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017)

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Components

#1: Protein Genome Polyprotein, capsid protein VP1 / EV71


Mass: 25347.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN0
#2: Protein Genome Polyprotein, capsid protein VP0 / EV71


Mass: 25987.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN0
#3: Protein Genome Polyprotein, capsid protein VP3 / EV71


Mass: 26125.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN0
Sequence detailsTHE AUTHORS INDICATE THAT BASED ON ELECTRON DENSITY MAPS, A225 IS MET.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM Ammonium phosphate monobasic, 24% (v/v) Isopropanol and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 69774 / % possible obs: 92.6 % / Observed criterion σ(I): -1.5 / Redundancy: 3.1 % / Rmerge(I) obs: 0.437 / Net I/σ(I): 2.1
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 0.5 / Num. unique all: 6944 / % possible all: 93.8

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Processing

Software
NameClassification
GDAdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VBO

3vbo


Resolution: 3.8→49.7 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 30945.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED STRICT NCS CONSTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 675 1 %RANDOM
Rwork0.257 ---
obs0.257 67864 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.1157 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 113.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.57 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 3.8→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5397 0 0 0 5397
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.168
X-RAY DIFFRACTIONc_mcangle_it11.1116
X-RAY DIFFRACTIONc_scbond_it13.2712
X-RAY DIFFRACTIONc_scangle_it17.8620
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 109 1 %
Rwork0.338 10594 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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